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Open data
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Basic information
Entry | Database: PDB / ID: 1mk9 | ||||||
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Title | CRYSTAL STRUCTURE OF AN INTEGRIN BETA3-TALIN CHIMERA | ||||||
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![]() | STRUCTURAL PROTEIN / FOCAL ADHESION / INTEGRIN BINDING / FERM DOMAIN / CYTOSKELETON NPXY MOTIF / PTB DOMAIN | ||||||
Function / homology | ![]() tube development / regulation of serotonin uptake / positive regulation of adenylate cyclase-inhibiting opioid receptor signaling pathway / alpha9-beta1 integrin-ADAM8 complex / regulation of trophoblast cell migration / regulation of postsynaptic neurotransmitter receptor diffusion trapping / alphav-beta3 integrin-vitronectin complex / regulation of extracellular matrix organization / platelet alpha granule membrane / positive regulation of glomerular mesangial cell proliferation ...tube development / regulation of serotonin uptake / positive regulation of adenylate cyclase-inhibiting opioid receptor signaling pathway / alpha9-beta1 integrin-ADAM8 complex / regulation of trophoblast cell migration / regulation of postsynaptic neurotransmitter receptor diffusion trapping / alphav-beta3 integrin-vitronectin complex / regulation of extracellular matrix organization / platelet alpha granule membrane / positive regulation of glomerular mesangial cell proliferation / integrin alphav-beta3 complex / negative regulation of lipoprotein metabolic process / alphav-beta3 integrin-PKCalpha complex / fibrinogen binding / maintenance of postsynaptic specialization structure / alphav-beta3 integrin-HMGB1 complex / blood coagulation, fibrin clot formation / negative regulation of lipid transport / vascular endothelial growth factor receptor 2 binding / glycinergic synapse / negative regulation of low-density lipoprotein receptor activity / angiogenesis involved in wound healing / Elastic fibre formation / regulation of release of sequestered calcium ion into cytosol / mesodermal cell differentiation / cell-substrate junction assembly / alphav-beta3 integrin-IGF-1-IGF1R complex / platelet-derived growth factor receptor binding / filopodium membrane / extracellular matrix binding / regulation of postsynaptic neurotransmitter receptor internalization / positive regulation of fibroblast migration / positive regulation of vascular endothelial growth factor receptor signaling pathway / apolipoprotein A-I-mediated signaling pathway / regulation of bone resorption / apoptotic cell clearance / positive regulation of cell adhesion mediated by integrin / wound healing, spreading of epidermal cells / heterotypic cell-cell adhesion / integrin complex / Molecules associated with elastic fibres / positive regulation of cell-matrix adhesion / cellular response to insulin-like growth factor stimulus / smooth muscle cell migration / microvillus membrane / negative chemotaxis / cell adhesion mediated by integrin / Syndecan interactions / p130Cas linkage to MAPK signaling for integrins / activation of protein kinase activity / cellular response to platelet-derived growth factor stimulus / cell-substrate adhesion / protein disulfide isomerase activity / positive regulation of smooth muscle cell migration / positive regulation of osteoblast proliferation / TGF-beta receptor signaling activates SMADs / PECAM1 interactions / lamellipodium membrane / GRB2:SOS provides linkage to MAPK signaling for Integrins / negative regulation of macrophage derived foam cell differentiation / platelet-derived growth factor receptor signaling pathway / negative regulation of lipid storage / fibronectin binding / ECM proteoglycans / positive regulation of T cell migration / positive regulation of bone resorption / Integrin cell surface interactions / coreceptor activity / negative regulation of endothelial cell apoptotic process / positive regulation of substrate adhesion-dependent cell spreading / cell adhesion molecule binding / ruffle / positive regulation of endothelial cell proliferation / embryo implantation / positive regulation of endothelial cell migration / Integrin signaling / substrate adhesion-dependent cell spreading / cell-matrix adhesion / response to activity / Signal transduction by L1 / integrin-mediated signaling pathway / regulation of actin cytoskeleton organization / protein kinase C binding / positive regulation of smooth muscle cell proliferation / Signaling by high-kinase activity BRAF mutants / wound healing / MAP2K and MAPK activation / structural constituent of cytoskeleton / platelet activation / platelet aggregation / ruffle membrane / VEGFA-VEGFR2 Pathway / cell-cell adhesion / cellular response to mechanical stimulus / positive regulation of angiogenesis / Signaling by RAF1 mutants / Signaling by moderate kinase activity BRAF mutants / Paradoxical activation of RAF signaling by kinase inactive BRAF / Signaling downstream of RAS mutants / regulation of protein localization Similarity search - Function | ||||||
Biological species | ![]() ![]() ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | Garcia-Alvarez, B. / De Pereda, J.M. / Calderwood, D.A. / Ulmer, T.S. / Critchley, D. / Campbell, I.D. / Ginsberg, M.H. / Liddington, R.C. | ||||||
![]() | ![]() Title: Structural Determinants of Integrin Recognition by Talin Authors: Garcia-Alvarez, B. / de Pereda, J.M. / Calderwood, D.A. / Ulmer, T.S. / Critchley, D. / Campbell, I.D. / Ginsberg, M.H. / Liddington, R.C. | ||||||
History |
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Remark 999 | SEQUENCE AUTHORS INFORMED THAT THE SEQUENCE OF CHICKEN TALIN IS NOT AVAILABLE IN ANY REFERENCE ...SEQUENCE AUTHORS INFORMED THAT THE SEQUENCE OF CHICKEN TALIN IS NOT AVAILABLE IN ANY REFERENCE DATABASE. THE SEQUENCE HAS BEEN DESCRIBED IN THE PUBLICATION: HEMMINGS, L., REES, D.J.G., OHANIAN, V., BOLTON, S.J., GILMORE, A.P., PATEL, N., PRIDDLE, H., TREVITHICK, J.E., HYNES, R.O., & CRITCHLEY, D.R. (1996). TALIN CONTAINS THREE ACTIN-BINDING SITES EACH OF WHICH IS ADJACENT TO A VINCULIN-BINDING SITE. J. CELL SCI., 109, 2715-2726. |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 153.1 KB | Display | ![]() |
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PDB format | ![]() | 129.9 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 481.6 KB | Display | ![]() |
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Full document | ![]() | 517.1 KB | Display | |
Data in XML | ![]() | 33.8 KB | Display | |
Data in CIF | ![]() | 45.4 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 1mixSC ![]() 1mizC ![]() 1mk7C S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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4 | ![]()
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Unit cell |
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Components
#1: Protein/peptide | Mass: 1835.990 Da / Num. of mol.: 4 / Fragment: PARTIAL CYTOPLASMIC TAIL (Residues 739-750) Source method: isolated from a genetically manipulated source Details: Forms chimera with talin at the C-terminus / Source: (gene. exp.) ![]() ![]() ![]() #2: Protein | Mass: 22150.656 Da / Num. of mol.: 4 Fragment: F2 AND F3 SUBDOMAINS OF FERM DOMAIN (Residues 209-400) Source method: isolated from a genetically manipulated source Details: Forms chimera with Integrin Beta3 at the N-terminus Source: (gene. exp.) ![]() ![]() ![]() ![]() #3: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.21 Å3/Da / Density % sol: 44.39 % | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 8.6 Details: PEG 8000, MAGNESIUM CHLORIDE, TRIS-HCL, pH 8.6, VAPOR DIFFUSION, HANGING DROP, temperature 277K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 4 ℃ / pH: 7 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() |
Detector | Type: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: May 5, 2002 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.8→29.83 Å / Num. obs: 18904 / % possible obs: 91.8 % / Observed criterion σ(I): -3 / Redundancy: 3.11 % / Biso Wilson estimate: 28.3 Å2 / Rsym value: 0.09 / Net I/σ(I): 13 |
Reflection shell | Resolution: 2.8→2.9 Å / Mean I/σ(I) obs: 4 / % possible all: 94.5 |
Reflection | *PLUS Highest resolution: 2.8 Å / Num. measured all: 57904 / Rmerge(I) obs: 0.09 |
Reflection shell | *PLUS % possible obs: 94.5 % / Rmerge(I) obs: 0.307 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 1MIX Resolution: 2.8→29.83 Å / Rfactor Rfree error: 0.009 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 27.9626 Å2 / ksol: 0.315075 e/Å3 | ||||||||||||||||||||
Displacement parameters | Biso mean: 26.7 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.8→29.83 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.8→2.98 Å / Rfactor Rfree error: 0.027 / Total num. of bins used: 6
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Xplor file |
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Refinement | *PLUS Highest resolution: 2.8 Å / Lowest resolution: 30 Å / Rfactor Rfree: 0.324 / Rfactor Rwork: 0.239 | ||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||
Refine LS restraints | *PLUS
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